2022-10-23
Introduction
Study
Henrick et al. 2021: Bifidobacteria-mediated immune system imprinting early in life
- Investigation: The effects of bifidobacteria and HMO-utilization genes during the first months of life
- Methods: Longitudinal systems immunology analysis combined with metagenomic profiling
Focus in this data analysis:
- Shotgun metagenomic sequencing of longitudinal fecal samples of infants
Study design
Data
Two TSV files:
Methods
Tidying data
- Bin data by weeks
- For subplots: filter by ‘Vaginal’ or ‘C-section’ prior to binning
- Drop NAs
- Filter data for weeks and bacterial species
- Bifido heat map data: keep baby ID
- Remove data >24 weeks
- Clean up names
Raw data
Family meta data
## sample.id baby_id family_id gestational_age group sex ## 1 2600164312 360 167 280 Term 1 ## 2 2600100341 162 69 278 Term 0 ## 3 2600100455 285 140 273 Term 0
## mode_delivery Days_after_birth Month_of_life f__Methanobacteriaceae ## 1 Vaginal 0 0 0 ## 2 Planned_C-section 1 0 0 ## 3 Vaginal 1 0 0
## f__Actinomycetaceae f__Bifidobacteriaceae f__Candidatus_Nanopelagicaceae ## 1 0.03489 1.62129 0 ## 2 0.00188 0.42010 0 ## 3 0.00000 0.46499 0
Raw data
Bifido meta data
## sample.id baby_id family_id gestational_age group sex ## 1 2600164312 360 167 280 Term 1 ## 2 2600100341 162 69 278 Term 0 ## 3 2600100455 285 140 273 Term 0
## mode_delivery Days_after_birth Month_of_life g__Bifidobacterium ## 1 Vaginal 0 0 1.62129 ## 2 Planned_C-section 1 0 0.42010 ## 3 Vaginal 1 0 0.46499
## g__Bifidobacterium.s__Bifidobacterium_adolescentis ## 1 0.02872 ## 2 0.02965 ## 3 0.00147
Tidying data
Family data:
## weeks Methanobacteriaceae Actinomycetaceae Bifidobacteriaceae ## 1 1 0 0.03489 1.62129 ## 2 1 0 0.00188 0.42010 ## 3 1 0 0.00000 0.46499 ## 4 1 0 0.00000 0.25688 ## 5 1 0 0.01905 1.01351
Bifido data:
## weeks B_adolescentis B_angulatum B_animalis ## 1 1 0.02872 0 0.00000 ## 2 1 0.02965 0 0.01920 ## 3 1 0.00147 0 0.00000 ## 4 1 0.04929 0 0.00000 ## 5 1 0.02277 0 0.04185
Tidying data
Family vaginal data:
Filter for vaginal
## sample.id baby_id family_id gestational_age group sex mode_delivery ## 1 2600164312 360 167 280 Term 1 Vaginal ## 2 2600100455 285 140 273 Term 0 Vaginal ## 3 2600100500 23 21 278 Term 0 Vaginal
Bin by weeks and clean-up
## weeks Methanobacteriaceae Actinomycetaceae Bifidobacteriaceae ## 1 1 0 0.03489 1.62129 ## 2 1 0 0.00000 0.46499 ## 3 1 0 0.00000 1.05293
Same steps were performed with filtering for C-section
Tidying data
Bifido C-section data:
Filter for C-section
## sample.id baby_id family_id group sex mode_delivery ## 1 2600100341 162 69 Term 0 Planned_C-section ## 2 2600100458 276 137 Term 1 Planned_C-section ## 3 2600100460 270 135 Term 0 Planned_C-section
Bin by weeks and clean-up
## weeks B_adolescentis B_angulatum B_animalis ## 1 1 0.02965 0 0.01920 ## 2 1 0.04929 0 0.00000 ## 3 1 0.02277 0 0.04185
Same steps were performed with filtering for Vaginal
Tidying data
Bifido heatmap data: Keeping baby ID when binning
## weeks baby_id g__Bifidobacterium B_adolescentis ## 1 1 360 1.62129 0.02872 ## 2 1 162 0.42010 0.02965 ## 3 1 285 0.46499 0.00147 ## 4 1 276 0.25688 0.04929 ## 5 1 270 1.01351 0.02277 ## 6 1 174 95.79804 0.00000 ## 7 1 147 23.07769 0.00000 ## 8 1 138 0.30136 0.13661 ## 9 1 23 1.05293 0.00159 ## 10 1 382 0.00000 0.00000
Data analysis
Exploring the data:
- Change in gutmicrobes across 24 weeks
- Family level abundance
- Bifidobacterium species level abundance
- Bifidobacterium species level abundance by baby ID
Results
Family level abundance
Calculating the relative abundance at family level. Families with mean ≤ 2% were merged into ‘Other’
Family level abundance
Splitting the previous plot into Vaginal and C-section births
Bifido sp. level abundance
Calculating the relative abundance at Bifidobacterium species level. Species with mean ≤ 2% were merged into ‘Other’
Bifido sp. level abundance
Splitting the previous plot into Vaginal and C-section births
Bifido species across infants
Bifido species across infants
Discussion
Discussion
- Increase in Bacteroidaceae and Bifidobacteriaceae at family level after birth in the majority of newborns.
- This expansion most frequently involved B. longum, B. breve, and B. bifidum in the first week.
- Variation at family and bifidobacterium level between modes of birth
- Highly variable bifidobacterial expansion across infants
Impact?
- Potential to alter the trajectory of immune system development?